VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 20 2021 - 00:51:18 CST

Phillip,
  We have made changes to Multiseq that have addressed the issues
with STAMP on MacOS, however there is a problem that occurs on
64-bit Windows that I'm still working on tracking down.
I plan to make new test builds of VMD in early January, possibly
even before then, and I'll let you know what the status of STAMP is
at that point.

Best,
  John

On Fri, Dec 17, 2021 at 11:58:45AM -0600, Phillip Compeau wrote:
> Hi John,
>
> Just letting you know that my course is now published at
> [1]https://biologicalmodeling.org. Please let me know when you think
> there's a fix to multiseq. As of the moment, I'm indicating that stamp
> alignment isn't working on the appropriate page.
>
> Thanks!
>
> Phillip
>
> On 12/3/21 9:22 AM, Phillip Compeau wrote:
>
> OK, thanks John!
>
> On 12/3/21 12:55 AM, John Stone wrote:
>
> Hi,
> Actually, in general it is best to post to the mailing list,
> because it often causes other users to comment about their
> experiences. In this case, your email caused someone else
> to report a different problem that also affected multiseq.
> If you hadn't posted to the mailing list, they may not have
> reported it. I'm thankful that they did, because we'll likely
> be able to fix both issues at the same time...
>
> Best,
> John Stone
>
>
> On Thu, Dec 02, 2021 at 05:16:11PM -0500, Phillip Compeau wrote:
>
> Hi John,
>
> Thanks so much for following up! In the meantime I will let students know
> that this is in the process of being fixed.
>
> Should I report any subsequent issues to you directly? I'm no longer
> CC-ing the mailing list to avoid clogging folks' inboxes.
>
> Phillip
>
> On 12/2/21 3:32 PM, John Stone wrote:
>
> Hi Phillip,
> We dug into the multiseq code today and indeed, there are some
> issues with it's conficting use of both "grid" and "pack" GUI layout
> managers that is almost certainly the cause of the hang you've seen.
>
> One of my colleagues here has volunteered to make an attempt at
> addressing these bugs since the original authors no longer
> support the code. I'm hoping we can have relatively rapid turnaround
> on a fix for this now that we've discovered some obvious underlying issues
> that need to be corrected.
>
> Best,
> John Stone
> [[2]1]vmd_at_ks.uiuc.edu
>
> On Wed, Dec 01, 2021 at 12:42:12AM -0600, John Stone wrote:
>
> Hi,
> I'm guessing that this hang is caused by some bug in the multiseq
> plugin related to its use of Tk, but that is only a guess.
> Do you see any error messages in the main VMD console associated
> with the hanging behavior, or is the hang the only observable behavior?
>
> Best,
> John Stone
> [[3]2]vmd_at_ks.uiuc.edu
>
> On Fri, Nov 26, 2021 at 11:05:02PM -0500, Phillip Compeau wrote:
>
> Hi,
>
> I am integrating VMD into a publicly available assignment that I
> provide to my course as well ([3][4]https://urldefense.com/v3/__https://compeau.cbd.cmu.edu/online-education/sars-cov-2-protein-analysis-assignment/__;!!DZ3fjg!pDclAv9hZA92L09-ahO0FM6uDcyFOGbfeoCQpKkV1Rz8lrsqL5MxWaVg_EjA4Hs4cg$
> ).
>
> As part of this, students are asked to, in the MultiSeq window,
> select Tools -> STAMP alignment options -> ok to perform a STAMP
> alignment with the default settings. However, this freezes for my
> students. At first I thought this was Windows only but it seems to
> affect both Windows and Mac.
>
> Thanks for your help! I'm not sure where else would make sense to
> report this issue.
>
> Regards,
>
> Phillip Compeau
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [4][5]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [5][6]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. [7]mailto:vmd_at_ks.uiuc.edu
> 2. [8]mailto:vmd_at_ks.uiuc.edu
> 3. [9]https://urldefense.com/v3/__https://compeau.cbd.cmu.edu/online-education/sars-cov-2-protein-analysis-assignment/__;!!DZ3fjg!pDclAv9hZA92L09-ahO0FM6uDcyFOGbfeoCQpKkV1Rz8lrsqL5MxWaVg_EjA4Hs4cg$
> 4. [10]http://www.ks.uiuc.edu/~johns/
> 5. [11]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. https://urldefense.com/v3/__https://biologicalmodeling.org__;!!DZ3fjg!us8dKpenTEr3SJAk2wpC9VONEjKxLHoltzlMXkkccxHGhoz20WVC-pXQqdIrZgBn$
> 2. mailto:1]vmd_at_ks.uiuc.edu
> 3. mailto:2]vmd_at_ks.uiuc.edu
> 4. https://urldefense.com/v3/__https://compeau.cbd.cmu.edu/online-education/sars-cov-2-protein-analysis-assignment/__;!!DZ3fjg!pDclAv9hZA92L09-ahO0FM6uDcyFOGbfeoCQpKkV1Rz8lrsqL5MxWaVg_EjA4Hs4cg$
> 5. http://www.ks.uiuc.edu/~johns/
> 6. http://www.ks.uiuc.edu/Research/vmd/
> 7. mailto:vmd_at_ks.uiuc.edu
> 8. mailto:vmd_at_ks.uiuc.edu
> 9. https://urldefense.com/v3/__https://compeau.cbd.cmu.edu/online-education/sars-cov-2-protein-analysis-assignment/__;!!DZ3fjg!pDclAv9hZA92L09-ahO0FM6uDcyFOGbfeoCQpKkV1Rz8lrsqL5MxWaVg_EjA4Hs4cg$
> 10. http://www.ks.uiuc.edu/~johns/
> 11. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/